Free Energy Landscape of a DNA-Carbon Nanotube Hybrid Using Replica Exchange Molecular Dynamics

The DNA-carbon nanotube hybrid (DNA-CN) consists of a single-wall carbon nanotube (SWCN) coated with a self-assembled monolayer of single-stranded DNA (ssDNA). Recent experiments have demonstrated that this nanomaterial is ideal for numerous nanotechnological applications. Despite this importance, the structure of this material remains poorly understood. Molecular dynamics (MD) simulations have provided information about the self-assembly mechanisms and ssDNA conformations that characterize DNA-CN. However, MD simulations of biopolymers at low temperatures (T similar to 300 K) result in kinetic trapping that limits conformational sampling. Here, we present results of a large-scale replica exchange molecular dynamics (REMD) simulation that provides extensive sampling of the entire ensemble of oligonucleotide conformations in a (GT)gamma-SWCN hybrid. We calculate the free energy landscape and find minima corresponding to six distinct conformations, with a nonhelical loop structure as the global minimum. The hybrid contains significant structural disorder, with desorbed bases as an important structural feature. These results expand our understanding of DNA-CN and indicate the relevance of REMD for explorations of the physical properties of organic-inorganic multifunctional nanomaterials.